Re: [Gusdev-gusdev] everything works except commit!

[MICHAEL L. <lu...@cs...>]

Hello Sucheta-
No. the plugin will not work with the raw blast output.  You must parse it
using a script such as parseBlastFilesForSimilarity.pl
which puts it in the format:
Cutoff parameters:
        P value: 1e-05
        Length: 10
        Percent Identity: 20

>383609 (96 subjects)
  Sum: 384224:3658:0.:16:2169:14:2163:2:3583:1525:2039:0:
   HSP1: 384224:905:1236:2247:3658:0.:16:2136:14:2135:0:
   HSP2: 384224:620:803:1336:2695:2.8e-282:884:2169:892:2163:0:
  Sum: 384422:3445:0.:1:2193:1:2163:2:2258:1076:1337:0:
   HSP1: 384422:800:986:1652:3445:0.:616:2193:586:2163:0:
   HSP2: 384422:276:351:606:1201:0.:1:575:1:576:0:
  Sum: 383758:3124:0.:3:2203:5:2163:4:4205:1809:2322:0:
   HSP1: 383758:773:977:1701:3124:0.:570:2180:555:2150:0:
   HSP2: 383758:601:794:1569:1928:0.:718:2203:692:2163:0:
   HSP3: 383758:259:314:494:1191:0.:3:473:5:481:0:
   HSP4: 383758:176:237:441:708:0.:310:718:298:700:0:
  Sum: 385607:3061:0.:8:2231:14:2163:3:2833:1143:1528:0:
   HSP1: 385607:728:940:1653:3061:0.:600:2192:577:2147:0:
   HSP2: 385607:248:332:568:1046:0.:8:550:14:549:0:
   HSP3: 385607:167:256:612:353:3.2e-134:1654:2231:1613:2163:0:
  Sum: 388168:2786:0.:5:2223:9:2163:5:2775:1226:1578:0:
   HSP1: 388168:659:831:1446:2786:0.:821:2200:770:2150:0:
   HSP2: 388168:243:295:473:1114:0.:5:459:9:453:0:
   HSP3: 388168:133:169:326:538:0.:290:607:287:588:0:
   HSP4: 388168:113:186:376:445:4.8e-179:641:996:572:932:0:
   HSP5: 388168:78:97:154:317:0.:2073:2223:2026:2163:0:
.
.
.
.


Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Mon, 19 Apr 2004, Sucheta Tripathy wrote:

> Hi Michael,
>
> I have not worked with the plugin yet, but just curious to know what input
> file type did you provide? Is it the raw blast output?
>
> Thanks
>
> Sucheta
>
> > Hello everyone-
> > I have been attempting to load blast similarities into GUS with the plugin
> > LoadBlastSimFast.pm after already loading some data in with the plugin
> > LoadBlastSimilarityPK.pm (which was slow compared with the Fasst version).
> > Well, the first thing that LoadBlastSimFast.pm does is start complaining
> > about PrimaryKey uniqueness constraints being violated.  It used some
> > fancy Oracle SQL that I didn't understand:
> > select dots.similarity_SQ.NEXTVAL from DUAL
> > Which by debugging I found out started at one, and increased each time we
> > tested the plugin, regardless of commit not being turned on.  Naturally
> > this crashed, because
> > we already had about 3,000 entries in the dots.similarity table and
> > we already had a sequence_id with value 1.  There
> > was likewise a problem with the dots.similarityspan table.
> >
> > Since I only having a workingman's knowledge of OracleSQL, I switched it
> > so that it starts with
> > select count(*) from dots.similarity
> > And increases this by one for each entry.  Likewise for
> > dots.similarityspan.  This seemed to fix the problem, and the plugin works
> > great on each file tested, claims to have entered all the correct data,
> > and exits gracefully.  Yet when I run the same command line with --commit
> > appended to the end, we start getting these Primary Key constraints
> > violated errors again.
> >
> > Perhaps I do not understand what happens with commit.  I thought that
> > these kind of errors would be caught with a regular run without commit
> > turned on.
> > Any help?
> >
> >
> >
> >
> > Michael Luchtan
> > http://www.cs.uga.edu/~luchtan
> >
> >
> >
> >
> >
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>
>
> --
> Sucheta Tripathy
> Virginia Bioinformatics Institute Phase-I
> Washington street.
> Virginia Tech.
> Blacksburg,VA 24061-0447
> phone:(540)231-8138
> Fax:  (540) 231-2606
>